Dear everyone,
I have a dimer composed of Chain B and Chain C (both chains were defined
as receptor and ligand separately), and I want to use alanine scanning
to asses the contribution to the dimer formation of some residues reside
on the dimer interface.
Firstly, I use the newest version of the MMPBSA.py. When I mutate 2
resides (one in receptor and one in ligand), then error happed as below:
MMPBSA.py -i mmpbsa.in -o mmpbsa.out -sp ../B_C.prmtop -cp
../B_C_pr.prmtop -rp ../B_pr.prmtop -lp ../C_pr.prmtop -y ../md6-10.crd
-mc B_C_mut.prmtop -mr B_mut.prmtop -ml C_mut.prmtop
ptraj found! Using /home/zjxu/project/prog/amber9/exe/ptraj
sander found! Using /home/zjxu/project/prog/amber9/exe/sander
Assuming /home/zjxu/project/prog/amber9/exe/sander is part of
amber9 or amber10. Using old PB input file.
Warning: igb=5 should be used with either mbondi2 or bondi pbradii set.
Yours are modified Bondi radii (mbondi)
Checking mutant topology files...
Error: More than one mutated residue!
Error: Invalid alanine scanning topology file(s)!
NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
However, when I mutate just one residue, then the process can be
completed rightly.
And I tried mm_pbsa.pl when mutate 2 residues, and everything is OK.
So I have a doubt that could MMPBSA.py mutate more than 1 residue?
I used amber9 and have applied all the patches for amber9 and MMPBSA.py.
The mmpbsa.in for MMPBSA.py is as below:
sample input file for running alanine scanning
&general
startframe=1, endframe=5000, interval=5,
verbose=1,
/
&gb
saltcon=0.1
/
&pb
istrng=0.100
/
&alanine_scanning
/
thanks for your time
Best Regards,
Zhijian Xu
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Received on Wed Dec 08 2010 - 23:30:03 PST
